// Created by Prof. Julian Sosnik for Prof. Catherine McCusker's Lab
// evolved from a macro created by Dr. Matheus Viana / Dr. Susanne Rafelski
//
//This work is distributed under the Modified BSD license (https://opensource.org/licenses/BSD-3-Clause)
//
///////////////////////////////////////////////////////////////////////////
//This macro opens a file, let's you select an area and then creates a cropped version 
// of your image (or stack, or Hyperstack) that contains only the portion
// of the original image that you selected...
// In the case of multiple channels, it generates sub-folders
// for each of the channels and stores the images there
//////////////////////////////////////////////////////////////////////////
run("Open...");
// gather file name and path for the original image
path = getInfo("image.directory");
name = getTitle();
l = lengthOf(name);
newName = substring(name,0,l-4);
getDimensions(width, height, channels, slices, frames);
File.makeDirectory(path+newName); //creates folder to save the output files

//select area to crop into new image
waitForUser("Select area to crop and hit ok");

///  Add selection to ROI manager to use later
roiManager("reset");
setOption("Show All", false)
if (selectionType() == -1){  //  Checks to see if there is a selection made to make an ROI
	makeRectangle(0, 0, width, height);  // If there is not one, it makes one with the dimensions of the whole image
} 

roiManager("add");
roiManager("remove slice info");
Roi.getBounds(roix, roiy, roiWidth, roiWeight);

setBatchMode(true);  // runs in background to accelerate process
setBatchMode("hide");


chan = channels;
if (chan>1){
	run("Split Channels");
}
for (ii=1; ii<=chan; ii++){
	File.makeDirectory(path+newName+"/C"+ii); //creates sub-folder to save the output files for each channel
	if (chan>1){
		orig = "C"+ii+"-"+name; // now can refer to that image as "orig"
	} else {
		orig = name;
	}
	selectImage(orig);    //select the image from the channel ii
	// gather information about the original image
	info = getMetadata("Info");
	getDimensions(width, height, channels, slices, frames);
	getVoxelSize(Vwidth, Vheight, depth, unit);
	fps = Stack.getFrameInterval();
	
	//make a new image z-stack
	newImage("C"+ii+"-"+newName+"_cropped", "16-bit Black", roiWidth, roiWeight, slices);
	final = getImageID;	//now can refer to this new z-stack as "final" and go back and forth between orig and final
	setMetadata("Info", info);
	run("Properties...", "channels="+channels+" slices="+slices+" frames="+frames+" unit="+unit+" pixel_width="+Vwidth+" pixel_height="+Vheight+" voxel_depth="+depth+" frame=["+fps+" sec]");
	Stack.setFrameRate(fps);
	
	//paste selection into the new stack frame by frame
	for (n=1; n<=slices; n++) {
		selectImage(orig);
		setSlice(n);
		roiManager("select", 0); //  Apply the ROI from the original image
		run("Copy");
		selectImage(final);
		setSlice(n);
		run("Paste");
	}
	selectImage(orig);
	close();
	selectImage(final);
	namefinal = "C"+ii+"-"+newName+"_cropped";
	save(path+newName+"/"+namefinal+".tif");  //saves cropped image
	//separates the slices into individual images
	run("Stack to Images");
	for (i=1; i<=slices; i++){
		j = IJ.pad(i, 4);
		imag = namefinal+"-"+j;
		selectImage(imag);
		na = getTitle();
		save(path+newName+"/C"+ii+"/"+na+".tif");
		close();
	}
}


//// Cleanup
roiManager("reset");
selectWindow("ROI Manager"); 
run("Close"); 

////// THE CODE ENDS HERE, NEXT LINE IS SO YOU KNOW WHEN THE PROGRAM IS DONE RUNNING
waitForUser("Done");  // Exit message